Related papers: Classifying Tree Topologies along Tropical Line Se…
Let $p',q'\in R^n$. Write $p'\sim q'$ if $p'-q'$ is a multiple of $(1,\ldots,1)$. Two different points $p$ and $q$ in $R^n/\sim$ uniquely determine a tropical line $L(p,q)$, passing through them, and stable under small perturbations. This…
The main result of this paper is a formula for the limit cycle of a 1-parameter family of subvarieties of a tropical compactification, expressed in terms of tropical intersections. Our theorem generalizes results of…
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that…
Tree rearrangement operations typically induce a metric on the space of phylogenetic trees. One important property of these metrics is the size of the neighbourhood, that is, the number of trees exactly one operation from a given tree. We…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
This paper studies graphs that have two tree decompositions with the property that every bag from the first decomposition has a bounded-size intersection with every bag from the second decomposition. We show that every graph in each of the…
We show that the tropical projective Grassmannian of planes is homeomorphic to a closed subset of the analytic Grassmannian in Berkovich's sense by constructing a continuous section to the tropicalization map. Our main tool is an explicit…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
In this paper, we present a flexible and probabilistic framework for tracking topological features in time-varying scalar fields using merge trees and partial optimal transport. Merge trees are topological descriptors that record the…
The space T_{d,n} of n tropically collinear points in a fixed tropical projective space TP^{d-1} is equivalent to the tropicalization of the determinantal variety of matrices of rank at most 2, which consists of real d x n matrices of…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
We study the topological structure of random geometric forests $G$ in the Euclidean plane under mild assumptions: non-crossing edges, stationarity, and finite edge intensity. The framework covers a broad range of constructions, including…
We present an analysis of the topologies of a class of networks which are optimal in terms of the requirements of having as short a route as possible between any two nodes while yet keeping the congestion in the network as low as possible.…
The topological complexity of a path-connected space $X,$ denoted $TC(X),$ can be thought of as the minimum number of continuous rules needed to describe how to move from one point in $X$ to another. The space $X$ is often interpreted as a…
In this article, we will prove that the set of 4-dissimilarity vectors of n-trees is contained in the tropical Grassmannian G_{4,n}. We will also propose three equivalent conjectures related to the set of m-dissimilarity vectors of n-trees…
In this article, we look into the tree gonality of genus $3$ metric graphs $\Gamma$ which is defined as the minimum of degrees of all tropical morphisms from any tropical modification of $\Gamma$ to any metric tree. It is denoted by…
The asymmetric tropical distance is a distance measure on the tropical torus $\mathbb{R}^n/\mathbb{R}\mathbf{1}$ and in particular on the Bergman fan $B(K_N) \subseteq \mathbb{R}^{\binom{N}{2}}/\mathbb{R}\mathbf{1}$ of the complete…
We study anisotropic scaling limits of topological field theories using tropical geometry. The resulting topological field theories are characterized by foliated geometries and are invariant under foliation-preserving gauge transformations.…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
The tropical semiring (R, min, +) has enjoyed a recent renaissance, owing to its connections to mathematical biology as well as optimization and algebraic geometry. In this paper, we investigate the space of labeled n-point configurations…